Abstract Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.
Content Type Journal Article
Category Communication
Pages 1-7
DOI 10.1007/s10858-012-9677-7
Authors
Ye Tian, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Stanley J. Opella, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
Francesca M. Marassi, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
Jakob T. Nielsen, Hamid R. Eghbalnia, Niels Chr. Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise,...
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03-09-2012 09:16 AM
SHIFTX2: Chemical Shift Prediction
SHIFTX2 website
SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2011
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 23 May 2011</br>
Jakob T., Nielsen , Hamid R., Eghbalnia , Niels Chr., Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we...
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05-24-2011 10:02 PM
SHIFTX2: significantly improved protein chemical shift prediction
SHIFTX2: significantly improved protein chemical shift prediction
Abstract A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3Ã? smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more),...
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04-01-2011 09:31 PM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
Related Articles Protein secondary structure prediction using NMR chemical shift data.
J Bioinform Comput Biol. 2010 Oct;8(5):867-84
Authors: Zhao Y, Alipanahi B, Li SC, Li M
Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
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10-29-2010 07:05 PM
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of
Abstract NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures,...
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08-14-2010 04:19 AM
Chemical shift prediction in random coil peptides
Please check this program and let me know if it does work for your random coil peptides.
http://bloch.anu.edu.au/cgi-bin/shiftpred/shiftpred.cgi
Thank you,
Bogdan Bancia
bbancia@yahoo.com
Improved chemical shift prediction by Rosetta conformational sampling
Linear Mode
